Mapping multiple RNA modifications simultaneously by proximity barcode sequencing.

RNA is subject to a multitude of different chemical modifications that collectively represent the epitranscriptome. Individual RNA modifications including N6-methyladenosine (mA) on mRNA play essential roles in the posttranscriptional control of gene expression. Recent technological advances have enabled the transcriptome-wide mapping of certain RNA modifications, to reveal their broad relevance and characteristic distribution patterns.

Insights into the 5-Carboxamido-5-Formamido-2-Iminohydantoin Structural Isomerization Equilibria.

Exposure of DNA to oxidants results in modification of the electron-rich guanine heterocycle including formation of the mutagenic 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) lesion. Previously thought to exist solely as a pair of diastereomers, we found under biologically relevant conditions that 2Ih reversibly closes to a formerly hypothetical intermediate and opens into a newly discovered regioisomer. In a nucleoside model, only ∼80% of 2Ih existed as the structure studied over the last 20 years with significant isomeric products persisting in buffered aqueous solution.

Identification of the Major Product of Guanine Oxidation in DNA by Ozone.

Ozonolysis of guanosine formed the 5-carboxamido-5-formamido-2-iminohydantoin (2Ih) nucleoside along with trace spiroiminodihydantoin (Sp). On the basis of literature precedent, we propose an unconventional ozone mechanism involving incorporation of only one oxygen atom of O to form 2Ih with evolution of singlet oxygen responsible for Sp formation. The increased yield of Sp in the buffered O-stabilizing solvent DO, formation of 2Ih in a short oligodeoxynucleotide, and O-isotope labeling provided evidence to support this mechanism.

Collateral Damage Occurs When Using Photosensitizer Probes to Detect or Modulate Nucleic Acid Modifications.

Nucleic acids are chemically modified to fine-tune their properties for biological function. Chemical tools for selective tagging of base modifications enables new approaches; the photosensitizers riboflavin and anthraquinone were previously proposed to oxidize N -methyladenine (m A) or 5-methylcytosine (5mdC) selectively. Herein, riboflavin, anthraquinone, or Rose Bengal were allowed to react with the canonical nucleosides dA, dC, dG, and dT, and the modified bases 5mdC, m A, 8-oxoguanine (dOG), and 8-oxoadenine (dOA) to rank their reactivities.

Simple kinetics, assay, and trends for soil microbial catalases.

In this report, we expand upon the enzymology and ecology of soil catalases through development and application of a simple kinetic model and field-amenable assay based upon volume displacement. Through this approach, we (A) directly relate apparent Michaelis-Menten terms to the catalase reaction mechanism, (B) obtain upper estimates of the intrinsic rate constants for the catalase community (k), along with moles of catalase per 16S rRNA gene copy number, (C) utilize catalase specific activities (SAs) to obtain biomass estimates of soil and permafrost communities (LOD, ~10 copy number gdw), and (D) relate kinetic trends to changes in bacterial community structure. In addition, this novel kinetic approach simultaneously incorporates barometric adjustments to afford comparisons across field measurements.

Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert.

In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with being the numerically dominant genus.